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Saez-Rodriguez group

Systems biomedicine

Publications

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Publication year

OmniPath: integrated knowledgebase for multi-omics analysis.

Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J.

Nucleic acids research, 2026

doi:10.1093/nar/gkaf1126.

Interpretable inflammation landscape of circulating immune cells.

Jiménez-Gracia L, Maspero D, Aguilar-Fernández S, Craighero F, Boulougouri M, Ruiz M, Marchese D, Caratù G, Liñares-Blanco J, Berasategi M, Ramirez Flores RO, Sanzo-Machuca A, Corraliza AM, Tran HA, Normand R, Nestor J, Hong Y, Kole T, van der Velde P, Alleblas F, Pedretti F, Aterido A, Banchero M, Soriano G, Román E, van den Berge M, Salas A, Carrascosa JM, Fernández Nebro A, Domènech E, Cañete JD, Tornero J, Gisbert JP, Choy E, Girolomoni G, Siegmund B, Julià A, Serra V, Elosua R, Tejpar S, Vidal S, Nawijn MC, Gut I, Saez-Rodriguez J, Marsal S, Villani AC, Nieto JC, Heyn H.

Nature medicine, 2026

doi:10.1038/s41591-025-04126-3.

Publisher Correction: Interpretable inflammation landscape of circulating immune cells.

Jiménez-Gracia L, Maspero D, Aguilar-Fernández S, Craighero F, Boulougouri M, Ruiz M, Marchese D, Caratù G, Liñares-Blanco J, Berasategi M, Ramirez Flores RO, Sanzo-Machuca A, Corraliza AM, Tran HA, Normand R, Nestor J, Hong Y, Kole T, van der Velde P, Alleblas F, Pedretti F, Aterido A, Banchero M, Soriano G, Román E, van den Berge M, Salas A, Carrascosa JM, Fernández Nebro A, Domènech E, Cañete JD, Tornero J, Gisbert JP, Choy E, Girolomoni G, Siegmund B, Julià A, Serra V, Elosua R, Tejpar S, Vidal S, Nawijn MC, Gut I, Saez-Rodriguez J, Marsal S, Villani AC, Nieto JC, Heyn H.

Nature medicine, 2026

doi:10.1038/s41591-026-04223-x.

Multiomic integration reveals tumoral heterogeneity of lipid dependence within lethal group 3 medulloblastoma.

Bernardi F, Torrejon J, Basili I, Van Ommeren R, Marsaud V, Yu H, Talbot J, Souphron J, Indersie E, Forget A, Bonneau B, Massiot A, Alcazar C, Figeac L, Bonerandi E, Cancila G, Sirbu O, Yadav N, Mohanakrishnan D, Lombard B, Loew D, Poullet P, Liva S, Lovino M, Lin IH, Nakashima T, Gharsalli T, Nicolas PA, Yubuki N, Ribas RA, Colsch B, Chu-Van E, Castelli F, Sampaio JL, Leboucher S, Lasgi C, Besse L, Soler MN, Lo Re V, Planque N, Abeysundara N, Balin P, Wang H, Su H, Wu X, Cavalli FMG, Saulnier O, Ficarra E, Di Marcotullio L, Kumegawa K, Maruyama R, Kawauchi D, Picard D, Remke M, Riffaud L, Puiseux C, Bouchoucha Y, Huybrechts S, Simbozel M, Bourdeaut F, Varlet P, Puget S, Blauwblomme T, Andrianteranagna M, Planchon JM, Dugourd A, Saez-Rodriguez J, Barillot E, Servant N, Martignetti L, Rich J, Kool M, Pfister SM, Agnihotri S, Suzuki H, Fanjul M, Wang WJ, Tsai JW, Sun RC, Beccaria K, Dufour C, Sarry JE, Michealraj KA, Taylor MD, Ayrault O.

Cancer cell, 2026

doi:10.1016/j.ccell.2025.12.012.

Quantitative systems toxicology: modelling to mechanistically understand and predict drug safety.

Goldring CE, Russomanno G, Pin C, Trairatphisan P, Beattie KA, Fisher CP, Piñero J, Brennan RJ, Clausznitzer D, Copple IM, de Kok TM, Duckworth CA, Furlong LI, Füzi B, Gabor A, Gall L, Hengstler J, Hermjakob H, Hunter F, Jennen D, Koskinen M, Kunnen SJ, Lammens L, Lobentanzer S, Mohr M, Passini E, Pritchard DM, Malik-Sheriff RS, Rodríguez B, Rossman EI, Saez-Rodríguez J, Schmidt F, Sison-Young R, Soininen I, Turner S, van de Water B, van Hasselt JGC, Venezia F, Willy JA, Leishman DJ, Stevens JL, Laplanche L.

Nature reviews. Drug discovery, 2025

doi:10.1038/s41573-025-01308-z.

BioContextAI is a community hub for agentic biomedical systems.

Kuehl M, Schaub DP, Carli F, Heumos L, Hellmig M, Fernández-Zapata C, Kaiser N, Schaul J, Kulaga A, Usanov N, Scverse Community, Krebs CF, Panzer U, Bonn S, Lobentanzer S, Saez-Rodriguez J, Puelles VG.

Nature biotechnology, 2025

doi:10.1038/s41587-025-02900-9.

OmniPath: integrated knowledgebase for multi-omics analysis

Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J.

Preprint, 2025

doi:10.1101/2025.09.11.675512.

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

de Jong G, Memi F, Gracia T, Lazareva O, Gould O, Aivazidis A, Dave M, Zhang Q, Jensen M, Rifaioglu AS, Barros-Silva JD, Eckert S, Zhou D, Wood Y, Tuck E, Er S, Marshall H, Roberts K, Trinh AL, Rai S, Shaw T, Oszlanczi A, Powell H, Petryszak R, Katsirea Z, Mamun I, Mulas I, Quaegebeur A, Briggs M, Makarchuk S, Cox J, Lee JTH, Rueda L, Saraswat M, Bulstrode H, Young A, Patel M, Porter T, Prigmore E, Mall M, Saez-Rodriguez J, Briscoe J, Rowitch DH, Mair R, Behjati S, Stegle O, Bayraktar OA.

Preprint, 2025

doi:10.1101/2025.05.13.653495.

The microenvironment of ulcerated acral melanoma is characterised by an inflammatory milieu and an enhanced humoral immune response

Vázquez-Cruz ME, Basurto-Lozada P, Molina-Aguilar C, van Haastrecht B, Simonin-Wilmer I, Orozco-Ruiz S, Martinez-Said H, Álvarez-Cano A, García-Ortega DY, Ferreira I, Hidalgo-Miranda A, Hinojosa-Ugarte D, Tavares-de-la-Paz LA, Olguin JE, Salinas I, Rodríguez-Pérez A, Martínez-Gómez JM, van der Zee IT, Grimes DR, Saez-Rodriguez J, de la Cruz HV, Newton-Bishop JA, Bishop DT, Levesque MP, Possik PA, Adams DJ, Robles-Espinoza CD.

Preprint, 2025

doi:10.1101/2025.05.05.25325616.

Cold and hot fibrosis define clinically distinct cardiac pathologies.

Miyara S, Adler M, Umansky KB, Häußler D, Bassat E, Divinsky Y, Elkahal J, Kain D, Lendengolts D, Ramirez Flores RO, Bueno-Levy H, Golani O, Shalit T, Gershovits M, Weizman E, Genzelinakh A, Kimchi DM, Shakked A, Zhang L, Wang J, Baehr A, Petrover Z, Sarig R, Dorn T, Moretti A, Saez-Rodriguez J, Kupatt C, Tanaka EM, Medzhitov R, Krüger A, Mayo A, Alon U, Tzahor E.

Cell systems, 2025

doi:10.1016/j.cels.2025.101198.

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

Oliver AJ, Huang N, Li R, Bartolome-Casado R, Nilsen HR, Gudino V, Melon-Ardanaz CdIBe, Fitzpatrick MEB, Provine NM, Polanski K, Koplev S, Milchsack LM, Dann E, Predeus AV, Cakir B, To K, Prete M, Chapman JA, Masi AC, Stephenson E, Engelbert J, Lobentanzer S, Perera S, Richardson L, Kapuge R, Wilbrey-Clark A, Semprich CI, Moy M, Ellams S, Tudor CL, Joseph P, Garrido-Trigo A, Corraliza CdIBe, Oliver TR, Hook CE, Saez-Rodriguez J, James KR, Meyer KB, Mahbubani KT, Saeb-Parsy K, Zilbauer M, Hoivik ML, Baekkevold ES, Salas CdIBe, Stewart CJ, Berrington JE, Klenerman P, Haniffa M, Jahnsen FL, Elmentaite R, Teichmann SA.

Preprint, 2024

doi:10.1101/2024.10.11.614415.

Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.

Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J.

Nucleic acids research, 2024

doi:10.1093/nar/gkae388.

Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing

Tetzlaff SK, Reyhan E, Bengtson CP, Schroers J, Wagner J, Schubert MC, Layer N, Puschhof MC, Faymonville AJ, Drewa N, Pramatarov RL, Wissmann N, Alhalabi O, Heuer A, Sivapalan N, Campos J, Boztepe B, Scheck JG, Villa G, Schröter M, Sahm F, Forsberg-Nilsson K, Breckwoldt MO, Acuna C, Suchorska B, Heiland HD, Saez-Rodriguez J, Venkataramani V.

Preprint, 2024

doi:10.1101/2024.03.18.585565.

Metrics reloaded: recommendations for image analysis validation.

Maier-Hein L, Reinke A, Godau P, Tizabi MD, Buettner F, Christodoulou E, Glocker B, Isensee F, Kleesiek J, Kozubek M, Reyes M, Riegler MA, Wiesenfarth M, Kavur AE, Sudre CH, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Rädsch T, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Blaschko MB, Cardoso MJ, Cheplygina V, Cimini BA, Collins GS, Farahani K, Ferrer L, Galdran A, van Ginneken B, Haase R, Hashimoto DA, Hoffman MM, Huisman M, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Karthikesalingam A, Kofler F, Kopp-Schneider A, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Mattson P, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rajpoot N, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, van Smeden M, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Jäger PF.

Nature methods, 2024

doi:10.1038/s41592-023-02151-z.

Understanding metric-related pitfalls in image analysis validation.

Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Buettner F, Cardoso MJ, Cheplygina V, Chen J, Christodoulou E, Cimini BA, Farahani K, Ferrer L, Galdran A, van Ginneken B, Glocker B, Godau P, Hashimoto DA, Hoffman MM, Huisman M, Isensee F, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Kleesiek J, Kofler F, Kooi T, Kopp-Schneider A, Kozubek M, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rafelski SM, Rajpoot N, Reyes M, Riegler MA, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Yaniv ZR, Jäger PF, Maier-Hein L.

Nature methods, 2024

doi:10.1038/s41592-023-02150-0.

Microbiome-based risk prediction in incident heart failure: a community challenge

Erawijantari PP, Kartal E, Liñares-Blanco J, Laajala TD, Feldman LE, The FINRISK Microbiome DREAM Challenge and ML4Microbiome Communities, Carmona-Saez P, Shigdel R, Claesson MJ, Bertelsen RJ, Gomez-Cabrero D, Minot S, Albrecht J, Chung V, Inouye M, Jousilahti P, Schultz J, Friederich H, Knight R, Salomaa V, Niiranen T, Havulinna AS, Saez-Rodriguez J, Levinson RT, Lahti L.

Preprint, 2023

doi:10.1101/2023.10.12.23296829.

Democratizing knowledge representation with BioCypher.

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.

Nature biotechnology, 2023

doi:10.1038/s41587-023-01848-y.

Multiscale networks in multiple sclerosis

Kennedy KE, Kerlero de Rosbo N, Uccelli A, Cellerino M, Ivaldi F, Contini P, De Palma R, Harbo HH, Berge T, Bos SD, Høgestøl EA, Brune-Ingebretsen S, de Rodez Benavent S, Paul F, Brandt AU, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer SE, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Saez-Rodriguez J, Rinas M, Alexopoulos L, Andorra M, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Garcia-Ojalvo J, Villoslada P.

Preprint, 2023

doi:10.1101/2023.02.26.530153.

Predicting disease severity in Multiple Sclerosis using multimodal data and machine learning

Andorra M, Freire A, Zubizarreta I, de Rosbo NK, Bos SD, Rinas M, Høgestøl EA, Benavent SAR, Berge T, Brune-Ingebretse S, Ivaldi F, Cellerino M, Pardini M, Vila G, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer S, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Brandt A, Saez-Rodriguez J, Alexopoulos L, Paul F, Harbo HF, Shams H, Oksenberg J, Uccelli A, Baeza-Yates R, Villoslada P.

Preprint, 2023

doi:10.21203/rs.3.rs-2414345/v1.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, de Leon MP, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Pinero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Cristobal MGL, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, the COVID-19 Disease Map Community.

Preprint, 2022

doi:10.1101/2022.12.17.520865.

Spatial cell type mapping of multiple sclerosis lesions

Lerma-Martin C, Badia-i-Mompel P, Ramirez Flores RO, Sekol P, Hofmann A, Thäwel T, Riedl CJ, Wünnemann F, Ibarra-Arellano MA, Trobisch T, Eisele P, Schapiro D, Haeussler M, Hametner S, Saez-Rodriguez J, Schirmer L.

Preprint, 2022

doi:10.1101/2022.11.03.514906.

Adult human kidney organoids originate from CD24<sup>+</sup> cells and represent an advanced model for adult polycystic kidney disease.

Xu Y, Kuppe C, Perales-Patón J, Hayat S, Kranz J, Abdallah AT, Nagai J, Li Z, Peisker F, Saritas T, Halder M, Menzel S, Hoeft K, Kenter A, Kim H, van Roeyen CRC, Lehrke M, Moellmann J, Speer T, Buhl EM, Hoogenboezem R, Boor P, Jansen J, Knopp C, Kurth I, Smeets B, Bindels E, Reinders MEJ, Baan C, Gribnau J, Hoorn EJ, Steffens J, Huber TB, Costa I, Floege J, Schneider RK, Saez-Rodriguez J, Freedman BS, Kramann R.

Nature genetics, 2022

doi:10.1038/s41588-022-01202-z.

Community assessment of methods to deconvolve cellular composition from bulk gene expression

White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S, Tumor Deconvolution DREAM Challenge consortium, Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ.

Preprint, 2022

doi:10.1101/2022.06.03.494221.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community.

Molecular systems biology, 2021

doi:10.15252/msb.202110387.

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community.

Molecular systems biology, 2021

doi:10.15252/msb.202110851.

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.

Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ.

Frontiers in microbiology, 2021

doi:10.3389/fmicb.2021.635781.

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M.

Bioinformatics (Oxford, England), 2021

doi:10.1093/bioinformatics/btaa622.

Decoding myofibroblast origins in human kidney fibrosis.

Kuppe C, Ibrahim MM, Kranz J, Zhang X, Ziegler S, Perales-Patón J, Jansen J, Reimer KC, Smith JR, Dobie R, Wilson-Kanamori JR, Halder M, Xu Y, Kabgani N, Kaesler N, Klaus M, Gernhold L, Puelles VG, Huber TB, Boor P, Menzel S, Hoogenboezem RM, Bindels EMJ, Steffens J, Floege J, Schneider RK, Saez-Rodriguez J, Henderson NC, Kramann R.

Nature, 2020

doi:10.1038/s41586-020-2941-1.

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

Douglass EF, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-i-Mompel P, Mateo L, Guitart-Pla O, Chung V, DREAM CTD-squared Pancancer Drug Activity Challenge Consortium, Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A.

Preprint, 2020

doi:10.1101/2020.12.21.423514.

Spatial multi-omic map of human myocardial infarction

Kuppe C, Ramirez Flores RO, Li Z, Hannani M, Tanevski J, Halder M, Cheng M, Ziegler S, Zhang X, Preisker F, Kaesler N, Xu Y, Hoogenboezem RM, Bindels EM, Schneider RK, Milting H, Costa IG, Saez-Rodriguez J, Kramann R.

Preprint, 2020

doi:10.1101/2020.12.08.411686.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Cristóbal Monraz Gómez L, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Leon MPd, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker J, Zucker J, Oxford K, Teuton J, Kocakaya E, Yağmur Summak G, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Ribeiro AS, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, Waard Ad, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Medina ME, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, Meulder BD, Dugourd A, Naldi A, Noë V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, the COVID-19 Disease Map Community.

Preprint, 2020

doi:10.1101/2020.10.26.356014.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Level 3 Community members.

Molecular systems biology, 2020

doi:10.15252/msb.20199110.

DreamAI: algorithm for the imputation of proteomics data

Ma W, Kim S, Chowdhury S, Li Z, Yang M, Yoo S, Petralia F, Jacobsen J, Li JJ, Ge X, Li K, Yu T, Calinawan AP, Edwards N, Payne SH, Boutros PC, Rodriguez H, Stolovitzky G, Zhu J, Kang J, Fenyo D, Saez-Rodriguez J, Wang P.

Preprint, 2020

doi:10.1101/2020.07.21.214205.

PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix

Kay EJ, Paterson K, Domingo CR, Sumpton D, Daebritz H, Tardito S, Boldrini C, Hernandez-Fernaud JR, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson LJ, Lilla S, Hedley A, Koulouras G, McGregor G, Jamieson C, Johnson RM, Park M, Kirschner K, Kirschner K, Miller C, Kamphorst JJ, Loayza-Puch F, Saez-Rodriguez J, Mazzone M, Blyth K, Zagnoni M, Zanivan S.

Preprint, 2020

doi:10.1101/2020.05.30.125237.

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Touré V, Vercruysse S, Acencio ML, Lovering R, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Licata L, Lægreid A, Mungall C, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Thieffry D, Thomas P, Türei D, Saez-Rodriguez J, Kuiper M.

Preprint, 2020

doi:10.20944/preprints202004.0480.v1.

Metabolic rewiring of the hypertensive kidney.

Rinschen MM, Palygin O, Guijas C, Palermo A, Palacio-Escat N, Domingo-Almenara X, Montenegro-Burke R, Saez-Rodriguez J, Staruschenko A, Siuzdak G.

Science signaling, 2019

doi:10.1126/scisignal.aax9760.

The authors reply.

Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R.

Kidney international, 2019

doi:10.1016/j.kint.2019.09.011.

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R.

iScience, 2019

doi:10.1016/j.isci.2019.10.059.

Predicting cellular position in the <i>Drosophila</i> embryo from Single-Cell Transcriptomics data

Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Glaab E, Krause R, Banda P, DREAM SCTC Consortium, Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P.

Preprint, 2019

doi:10.1101/796029.

MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis.

Kotelnikova E, Kiani NA, Messinis D, Pertsovskaya I, Pliaka V, Bernardo-Faura M, Rinas M, Vila G, Zubizarreta I, Pulido-Valdeolivas I, Sakellaropoulos T, Faigle W, Silberberg G, Masso M, Stridh P, Behrens J, Olsson T, Martin R, Paul F, Alexopoulos LG, Saez-Rodriguez J, Tegner J, Villoslada P.

Proceedings of the National Academy of Sciences of the United States of America, 2019

doi:10.1073/pnas.1818347116.

Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M, Ansari R, Harper S, Jackson DA, McRae R, Pooley R, Wilkinson P, van der Meer D, Dow D, Buser-Doepner C, Bertotti A, Trusolino L, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ.

Nature, 2019

doi:10.1038/s41586-019-1103-9.

Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, The DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D, Aicheler F, Amoroso N, Arenas A, Azhagesan K, Baker A, Banf M, Batzoglou S, Baudot A, Bellotti R, Bergmann S, Boroevich KA, Brun C, Cai S, Caldera M, Calderone A, Cesareni G, Chen W, Chichester C, Choobdar S, Cowen L, Crawford J, Cui H, Dao P, Domenico MD, Dhroso A, Didier G, Divine M, Sol Ad, Fang T, Feng X, Flores-Canales JC, Fortunato S, Gitter A, Gorska A, Guan Y, Guénoche A, Gómez S, Hamza H, Hartmann A, He S, Heijs A, Heinrich J, Hescott B, Hu X, Hu Y, Huang X, Hughitt VK, Jeon M, Jeub L, Johnson N, Joo K, Joung I, Jung S, Kalko SG, Kamola PJ, Kang J, Kaveelerdpotjana B, Kim M, Kim Y, Kohlbacher O, Korkin D, Krzysztof K, Kunji K, Kutalik Z, Lage K, Lamparter D, Lang-Brown S, Le TD, Lee J, Lee S, Lee J, Li D, Li J, Lin J, Liu L, Loizou A, Luo Z, Lysenko A, Ma T, Mall R, Marbach D, Mattia T, Medvedovic M, Menche J, Mercer J, Micarelli E, Monaco A, Müller F, Narayan R, Narykov O, Natoli T, Norman T, Park S, Perfetto L, Perrin D, Pirrò S, Przytycka TM, Qian X, Raman K, Ramazzotti D, Ramsahai E, Ravindran B, Rennert P, Saez-Rodriguez J, Schärfe C, Sharan R, Shi N, Shin W, Shu H, Sinha H, Slonim DK, Spinelli L, Srinivasan S, Subramanian A, Suver C, Szklarczyk D, Tangaro S, Thiagarajan S, Tichit L, Tiede T, Tripathi B, Tsherniak A, Tsunoda T, Türei D, Ullah E, Vahedi G, Valdeolivas A, Vivek J, Mering Cv, Waagmeester A, Wang B, Wang Y, Weir BA, White S, Winkler S, Xu K, Xu T, Yan C, Yang L, Yu K, Yu X, Zaffaroni G, Zaslavskiy M, Zeng T, Zhang JD, Zhang L, Zhang W, Zhang L, Zhang X, Zhang J, Zhou X, Zhou J, Zhu H, Zhu J, Zuccon G.

Preprint, 2018

doi:10.1101/265553.

Whither systems medicine?

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O.

Experimental & molecular medicine, 2018

doi:10.1038/emm.2017.290.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell reports, 2017

doi:10.1016/j.celrep.2017.08.010.

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA.

Oncogene, 2016

doi:10.1038/onc.2016.427.

A Landscape of Pharmacogenomic Interactions in Cancer.

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.

Cell, 2016

doi:10.1016/j.cell.2016.06.017.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nature methods, 2016

doi:10.1038/nmeth.3773.

DREAMTools: a Python package for scoring collaborative challenges.

Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.

F1000Research, 2015

doi:10.12688/f1000research.7118.2.

Prospective derivation of a living organoid biobank of colorectal cancer patients.

van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.

Cell, 2015

doi:10.1016/j.cell.2015.03.053.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nature biotechnology, 2014

doi:10.1038/nbt.2877.

Cellular Regulatory Networks

Joughin BA, Cheung E, Karuturi RKM, Saez-Rodriguez J, Lauffenburger DA, Liu ET.

2009

doi:10.1016/b978-0-12-372550-9.00004-3.

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